[RASMB] graphing AUC data

[Tara Suntoke]

Hi all,
I am fairly new to AUC and have a question about Sednterp and graphing AUC data.  

I spun a peptide that is a clean trimer- other people have published the same result for the same peptide.  I think the data is good for the following reasons:  the residuals are random, the data fits best to a single species, and has a square root of variance of 5.9 e-3.  In addition, the molecular weight I get from the experiment, (24.8kD for the trimer) is within 4.8% of the calculated MW in Sednterp (based on composition).  

I am trying to make a graph of ln(A) vs. r^2, and show that the peptide corresponds to a trimer and not a dimer or tetramer.  In order to graph the lines of the dimer, trimer, and tetramer, I used the equation of a line as follows:

ln(A) = (sigma)(r^2) + ln(A1).  I obtained the constant ln(A1) from the WinNonlin program. 

My question is about which value of sigma I should use.  I can use the value of sigma obtained from Nonlin, which is based on the data.  Alternatively, I can use the sigma that Sednterp gives me, based on the peptide composition and buffers.  When making these graphs however, the data fits exactly to the line for a trimer which uses the Nonlin sigma, and doesn't exactly follow the slope of the line that uses the Sednterp sigma.  I understand that the sigma obtained from Nonlin comes from the data, and perhaps that is why it fits to the data well.  On the other hand, the sigma from Sednterp is calculated using density and partial specific volumes that are close estimates, but aren't exact. (at least this is my understanding so far...)  So I am wondering which value of sigma is appropriate to use.

I'm not sure whether you will be able to see this at all, but I have enclosed a PDF to show you the different results I get using the different sigma values.  In all the papers that use the same peptide, people report graphs very similar to the lower one, which uses sigma derived from Nonlin.  The data always overlaps the line for a trimer.  However, it isn't clear how they generated those graphs. 

I would greatly appreciate any advice you have.

Thanks for your help,

Tara Suntoke
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